Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5210
Trapped Gene
Nufip2 (ENSMUSG00000037857)
Vector Insertion
Chr 11: 77500010 - 77505043
Public Clones (sanger) YTC023 (baygenomics) CSH498 (baygenomics) P135A03 (ggtc)
(ggtc) PST22409-NR (escells) IST12265G12 (tigm)
Private Clones OST340022 (lexicon) OST281070 (lexicon) OST63802 (lexicon)
Severity of mutation (?) Insertion after 13% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000292202 (Chr11:77499641..77500009 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGCAGCCTCACCAATACCTG Chr11:77499887..77499906 60.28 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000292202 (Chr11:77499641..77500009 +)
Downstram Exon
ENSMUSE00000292192 (Chr11:77505044..77506756 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGCAGCCTCACCAATACCTG Chr11:77499887..77499906 60.28 55 ATGGTGACACGGAGGAGTTC Chr11:77505898..77505917 59.97 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000292202 Chr11:77499641..77500009 AGCAGCCTCACCAATACCTG Chr11:77499887..77499906 60.28 55

*** Putative Vector Insertion (Chr 11: 77500010 - 77505043) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000292192 Chr11:77505044..77506756 ATGGTGACACGGAGGAGTTC Chr11:77505898..77505917 59.97 55
downstream ENSMUSE00000292185 Chr11:77519011..77519043 No primer for this exon
downstream ENSMUSE00000650373 Chr11:77523185..77524259 ATGAACGGTGGCTCTAATGC Chr11:77523293..77523312 60.1 50
downstream ENSMUSE00000650374 Chr11:77555188..77555294 ACCAATGTAACGCCAGTTCC Chr11:77555292..77555311 59.86 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTCTCCCTGCCCCTAATTTT Chr11:77502992..77503012 59.42 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTCTCCCTGCCCCTAATTTT Chr11:77502992..77503012 59.42 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037857